Checklist for release - Githubissues

alisterburt commented 2 years ago

This is an issue to track things that we consider essential before concluding this chapter

[ ] Check that TSA metadata is correctly generated from AreTomo alignment and can be used to reconstruct tomograms using RELION
[ ] Independent, easy to run installation checks for both AreTomo and IMOD
[ ] creating downsampled images for faster visualisation
[ ] interactive tilt-image exclusion job
[ ] Etomo launcher, allowing to further refine/optimise an IMOD tilt-series alignment
[ ] particle picking (simple points, dipoles, spheres, surfaces, filaments, tubes)
[ ] integrate everything into RELION GUI
[ ] add CCP-EM pipeliner job types

cc @EuanPyle

inter1965 commented 2 years ago

Are there patches for relion's motioncor & ctf estimation jobs?

EuanPyle commented 2 years ago

Yep, these are in the process of being implemented but aren't quite ready yet.

alisterburt commented 2 years ago

To clarify, there are already patches for motioncor, none for ctffind which is a simple wrapper around ctffind4

EuanPyle commented 2 years ago

Potential things to add: A flip YZ/Z option in Tomogram Reconstruction? Denoising option also in Tomogram Reconstruction (I'm exploring cryoCARE at the moment)

alisterburt commented 2 years ago

I think we should avoid adding options for flipping to minimise the number of ways handedness can be inverted, keep it simple :)

Denoising after reconstruction will be useful but I don't consider it essential for a first release, go ahead though!

inter1965 commented 2 years ago

How about multiple instance of aretomo when aligning tilt series? Currently there's no option to pass to "relion_run_align_tiltseries", is it possible to make it work as "relion_run_motioncorr" to use different GPU simultaneously?

alisterburt commented 2 years ago

@inter1965 there's an MPI runner inside relion for aligning tilt-series in parallel - I haven't tested it for AreTomo though. @EuanPyle might have more info?

EuanPyle commented 2 years ago

Must admit I never have used multi GPU to run AreTomo, it's developed by the same people so I imagine it's possible to run in the same way...I'll look into it

inter1965 commented 2 years ago

AreTomo has the same option "-Gpu" like MotionCor2 which specify which gpu to use, And there's also a "--gpu" option in relion's motioncor_runner (with or without _mpi) to specify "Device ids for each MPI-thread, e.g 0:1:2:3", however it lacks options to pass through between relion_run_align_tiltseries -> relion_tomo_align_tilt_series -> lil_aretomo -> aretomo.

EuanPyle commented 2 years ago

I see, I will add GPU specification to lil_aretomo/relion_tomo_align_tilt_series and will ask for that option to be put into rln if it doesn't exist already.

EuanPyle commented 2 years ago

This will be added to tomo_PP and lil_aretomo imminently :) still need to add to rln GUI though

EuanPyle commented 2 years ago

Forgot to update, this is working in tomo_PP and rln GUI as well. Currently number of GPUs must match number of MPI in rln so multiple GPUs aren't assigned to the same TS.

alisterburt commented 2 years ago

closing because development has moved to relion repo

alisterburt / tomo_preprocessing

Checklist for release #13